Contacts of the strand formed by residues 127 - 133 (chain C) in PDB entry 5KC6
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 127 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A THR* 5.4 0.2 + - - -
118C VAL* 4.3 14.8 - - + +
120C LYS* 3.6 37.5 - - + -
123C ASN* 4.7 0.7 - - - +
125C GLN 4.3 1.1 + - - +
126C THR* 1.3 79.2 - - - +
128C GLN* 1.3 63.4 + - - +
129C VAL* 4.3 10.8 - - + -
142C PHE* 3.7 6.9 - - - +
143C ALA* 3.3 35.3 + - + +
153C ALA* 4.5 4.3 - - + -
171C LEU* 4.0 6.3 - - + -
173C ARG* 3.4 17.0 - - - +
175C ASN 3.4 31.4 - - - +
176C LEU* 3.9 18.2 - - + -
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Residues in contact with GLN 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A TYR* 4.2 12.0 + - - -
127C ILE* 1.3 77.4 - - - +
129C VAL* 1.3 65.0 + - - +
130C SER* 4.1 4.4 + - - -
140C SER* 3.6 22.7 + - - -
141C ALA 3.4 8.5 - - - +
142C PHE* 3.3 32.7 - - + -
171C LEU* 3.6 2.9 - - - +
172C GLU* 2.7 48.7 + - + +
173C ARG* 3.3 28.8 + - + +
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Residues in contact with VAL 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C ILE* 3.6 34.1 - - + -
116C PHE* 3.7 28.5 - - + -
118C VAL* 3.8 25.6 - - + -
127C ILE* 4.3 4.0 - - + -
128C GLN* 1.3 76.1 - - - +
130C SER* 1.3 66.2 + - - +
140C SER* 3.2 3.3 - - - -
141C ALA* 2.8 34.4 + - - +
153C ALA* 4.3 10.1 - - + -
169C LEU* 4.2 11.0 - - + -
170C LYS 3.4 5.2 - - - +
171C LEU* 4.1 9.6 - - + -
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Residues in contact with SER 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C GLN* 4.1 0.9 + - - -
129C VAL* 1.3 75.7 - - - +
131C LEU* 1.3 61.8 + - - +
132C MET* 3.5 13.9 + - - +
137C PRO* 4.5 5.1 - - - +
139C ILE 3.2 7.2 - - - -
140C SER* 2.5 25.5 + - - -
169C LEU* 3.5 3.2 - - - -
170C LYS 3.0 31.8 + - - -
172C GLU* 2.9 37.1 + - - +
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Residues in contact with LEU 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C PHE* 3.8 26.2 - - + -
116C PHE* 4.1 13.1 - - + -
130C SER* 1.3 71.2 - - - +
132C MET* 1.3 66.9 + - - +
137C PRO* 3.6 1.4 - - - +
138C VAL* 2.8 40.9 + - + +
139C ILE* 2.9 26.1 + - + +
157C VAL* 3.6 31.2 - - + -
159C ILE* 4.8 4.9 - - + -
167C ALA* 4.8 4.0 - - + -
168C TYR 3.7 12.8 - - - +
169C LEU* 3.8 15.7 - - + +
185C PHE* 4.2 18.2 - - + -
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Residues in contact with MET 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C SER* 3.7 14.4 - - - +
131C LEU* 1.3 76.6 - - - +
133C LEU* 1.3 60.1 + - - +
134C ASN 4.1 0.9 - - - -
135C GLY* 4.3 6.3 - - - +
136C TRP 3.5 26.2 - - - -
137C PRO* 3.5 11.7 - - + -
138C VAL* 4.5 1.1 - - - -
166C ARG 3.5 0.4 - - - +
167C ALA* 3.3 9.4 - - - +
168C TYR* 2.7 69.7 + - + +
170C LYS* 3.9 25.6 - - + +
172C GLU* 3.3 38.4 - - - +
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Residues in contact with LEU 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C MET* 1.3 73.2 - - - +
134C ASN* 1.3 76.2 + - - +
135C GLY 3.3 0.4 - - - -
136C TRP* 2.7 28.9 + - + +
138C VAL* 3.7 18.6 - - + +
159C ILE* 4.2 18.4 - - + -
160C GLN 4.2 17.5 - - - +
161C MET* 3.9 17.0 - - + -
165C ASP* 3.9 28.5 - - + +
166C ARG 3.3 12.1 - - - +
167C ALA* 5.1 0.7 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il